NDM-1 Beta-lactamase Project

Edit 189 …
a.k.a. CRE (Carbapenem-Resistant Enterobacteriaceae)

Dr. B notes (090613)
Wet Lab stuff:
Nitrocefin is in. (2 vials of 5mg each)
- standard curve of varying amount of enzyme
- determine Km & kinetics

Graphpad prism login info (remote desktop using Windows - not sure if it will work from a Mac or Linux)
-- find remote desktop in Windows start menu from your computer and enter this info.
vdsstationpc.dyndns.org
username: vdsstationPC\vdsclass
passwerd: same as to get into laptops in lab

Alternatively, this is the computer outside of Dr. B’s office that you can go sit at.


Virtual Stuff




CDC page on CRE's: http://www.cdc.gov/hai/organisms/cre/

Link to Madeline's Mini-Research Write Up page: Beta Lactam resistant bacteria

PDB 'Featured System' page: http://sbkb.org/kb/featured_molecule_latest.html



VS4 Protocol (original)

LabVirtualScreen4_NDM-1_metalloBetaLactamase_VDS_Spring13.docx


VS4 Redo Protocol (version 3)

See: GDocs/Protocols/VirtualScreening/...

re-run the docking with the modifications made (if you didn't originally have a metal or a ligand - restart with a PDB structure that has a metal and a ligand in the active site)
post results in table below alongside your original VS4 results

VS4 Redo Again Protocol

same as above, but this time Delete the CONECT records to the Zincs (or any metals) in your PDB file after it has gone through Molprobity


INSTRUCTIONS:

  1. Choose which structure you will dock against. Fill in your name next to that entry. Only 5 researchers per target.
  2. Once you have completed docking, enter your results in Table 2. below.

Table 1. Associated PDB entries of crystal structures for NDM-1 beta-metallo lactamase
PDB ID:
 Description
 Researcher 1
 Researcher 2
 Researcher 3
 Researcher 4
 Researcher 5
4HKY
 New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem
 Alice C.
 Qasim A.
 Marianna U.
 Miguel T.
 Brandy C.
4HL1
 Crystal Structure of New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Ampicillin
 Aaron H.
 Grant T.
 Jensen G.
 Grayson N.
 Spencer C.
4HL2
 New Delhi Metallo-beta-Lactamase-1 1.05 A structure Complexed with Hydrolyzed Ampicillin (Metals were shown in PyMol, but not in GOLD)
 Julia C.
 Karuna A.
 Jacqueline E.
 Gabe H.
4GYQ
 Crystal Structure of New Delhi Metallo-beta-Lactamase-1 D223A mutant from Klebsiella pneumoniae-




4GYU
 Crystal Structure of New Delhi Metallo-beta-Lactamase-1 A121F mutant from Klebsiella pneumoniae-




4H0D
 New Delhi Metallo-beta-Lactamase-1 Complexed with Mn from Klebsiella pneumoniae




4EYB
 Crystal structure of NDM-1 bound to hydrolyzed oxacillin
 Caroline C.
 D'Ondria P.
 Kevin E.
 Shannon R.
 William I.
4EXS
 Crystal structure of NDM-1 bound to L-captopril
 Gautam W.
 Khady D.
 William E.
 Nicole W.
 Brendan C.
4EXY
 Crystal structure of NDM-1 bound to ethylene glycol
 Emily J.
 Nancy I.
 Alyssa K.
 Vicky G.
 Hyun-Young L.
4EY2
 Crystal structure of NDM-1 bound to hydrolyzed methicillin
 Tony G.
 Karinna L.
 Melissa H.
 Dax F.G.
 Ramiro R.
4EYF
 Crystal structure of NDM-1 bound to hydrolyzed benzylpenicillin
 Imran Zafar
 Feng G.
 Grace T.
 Daniel D.
 Nicolet F.
4EYL
 Crystal structure of NDM-1 bound to hydrolyzed meropenem
 Priya P.
 Jiaqi Z.
 Stella M.
 Selena I.
 Renee F.
3PG4
 The crystal structure of New Delhi Metallo-beta lactamase (NDM-1)




3SPU
 apo NDM-1 Crystal Structure-




3SRX
 New Delhi Metallo-beta-Lactamase-1 Complexed with Cd-




3SBL
 Crystal Structure of New Delhi Metal-beta-lactamase-1 from Klebsiella pneumoniae
 Jesus
DE La O
 James T.
 Alakh R
 Jessica N.
 Katherine V.
3SFP
 Crystal Structure of the Mono-Zinc-boundform of New Delhi Metallo-beta-Lactamase-1 from Klebsiella pneumoniae



3ZR9
 STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE 1 (NDM-1)-




3S0Z
 Crystal structure of New Delhi Metallo-beta-lactamase (NDM-1)-




3Q6X
 Crystal structure of NDM-1 in complex with hydrolyzed ampicillin
 Shivani B.
 Serena Z.
 Shawn O
 So-Youn P
 Anita V.
3RKJ
 Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pnueumoniae (no metal in active site- could not re-run VS4)
 Keely W.
 Aditi S.
 Kavya K.
 Min S.
 Ariel C.
3RKK
 Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pneumoniae-
 [[#|Seo]] Kelly K.




Table 2. Gold docking scores of various ligands against NDM-1 beta-metallo lactamase crystal sctructures (nonhis)
#
 RESEARCHER NAME
 PDB ID
 'POSITIVE' CTRL1
 Faropenem
-drug
 Penicillin
-drug
 Clavulanic Acid
-inhibitor
 Aspririn
-random
 Original Ligand
 '
(REDO redo)
POSITIVE' CTRL1
 (REDO redo)
Faropenem
-drug
 (REDO redo)
Penicillin
-drug
 (REDO redo)
Clavulanic Acid
-inhibitor
 (REDO redo)
Aspririn
-random
 (REDO redo)
Original Ligand
1
 Gautam W.
 4EXS
 79.39
 57.05
 70.08
 52.21
 50.05
 48.55





2
 Khady D.
 4EXS
 64.47
 73.75
 83.51
 72.77
 68.75
 69.83





3
 Nicole W.
 4EXS
 64.83
 72.19
 84.14
 70.06
 68.48
 69.07





4
 Jesus De
 3SBL
 49.51
 45.79
 42.19
 44.91
 40.97
 43.99





5
 Tony G.
 4EY2
 74.86
 77.57
 70.23
 65.34
 68.7
 80.27
 79.27
 81.04
 74.00
 70.93
 65.83
 84.15
6
 Shivani B.
 3Q6X
 80.35
 80.70
 76.71
 67.52
 69.72
 83.38





7
 Serena Z.
 3Q6X
 80.50
 81.35
 76.42
 67.86
 69.90
 84.17





8
 Shawn O.
 3Q6X
 80.44
 81.57
 77.31
 67.78
 72.22
 83.26





9
 William E.
 4EXS
 64.56
 58.59
 70.18
 53.04
 50.03
 49.58





10
 Imran Zafar
 4EYF
 76.66
 77.18
 72.53
 64.4
 67.15
 81.4





11
 Caroline C.
 4EYB
 74.96
 78.48
 70.76
 64.27
 67.00
 92.86





12
 Alice C.
 4HKY
 86.22
 74.46
 76.00
 66.42
 67.47
 77.17





13
 Keely W.
 3RKJ
 60.2
 42.1
 49.6
 36.2
 34.9
 10.7





14
 Grace T.
 4EYF
 75.67
 76.81
 72.89
 64.67
 67.19
 83.91





15
 Kavya K.
 3RKJ
 62.44
 41.00
 50.69
 37.24
 35.31
 11.45
 (no metal in active site- could not re-run VS4)
 NA
 NA
 NA
 NA
 NA
16
 Aaron Hong
 4HL1
 53.95
 81.18
 62.39
 73.67
 75.92
 83.60





17
 D'Ondria P.
 4EYB
 77.48
 88.22
 80.07
 70.88
 70.65
 84.19





18
 Nicolet F.
 4EYF
 73.29
 80.40
 76.36
 65.64
 69.17
 81.00
 71.96
 84.50
 79.23
 70.53
 80.28
 83.34
19
 Grayson N.
 4HL1
 61.99
 83.43
 77.54
 75.55
 75.66
 83.95





20
 Emily J.
 4EXY
 79.94
 74.34
 70.79
 74.22
 73.29
 38.68





21
 Katherine V.
 3SBL
 45.23
 43.29
 41.76
 44.03
 41.26
 44.41
 48.70
 42.78
 42.78
 45.21
 41.33
 44.95
22
 Marianna U.
 4HKY











23
 Jessica N.
 3SBL
 44.69
 46.04
 42.63
 44.92
 41.33
 44.37





24
 Karinna L.
 4EY2
 77.44
 78.61
 69.95
 65.41
 68.54
 78.45





25
 Grant T.
 4DHL1
 87.93
 81.35
 79.90
 75.43
 75.63
 87.95





26
 Kevin E.
 4EYB
 75.66
 77.78
 71.10
 64.73
 67.30
 89.56
 80.93
 80.38
 76.66
 69.89
 69.62
 87.91
27
 Alyssa K.
 4EXY
 74.16
 74.96
 70.23
 74.46
 73.41
 38.78
 81.32
 77.09
 73.95
 73.74
 73.76
 41.37
28
 Aditi S.
 3RKJ
 67.72
 57.63
 61.38
 55.15
 48.43
 23.76





29
 Qasim A.
 4HKY
 49.43
 75.32
 73.16
 65.18
 67.27
 69.1





30
 Julia C.
 4HL2
 79.93
 80.14
 79.46
 69.94
 66.06
 82.59





31
 Feng G.
 4EYF
 74.74
 79.93
 76.12
 65.54
 69.33
 83.12





32
 Min S.
 3RKJ
 65.13
 55.55
 52.15
 51.48
 43.23
 25.23





33
 Melissa H.
 4EY2
 74.67
 79.04
 70.34
 65.31
 65.98
 78.62
 78.73
 84.20
 77.53
 70.16
 71.03
 84.68
34
 Shannon R.
 4EYB
 76.96
 76.40
 75.45
 64.53
 67.12
 91.53





35
 Anita V.
 3Q6X
 75.69
 53.73
 50.68
 35.44
 36.04
 58.87





36
 Marianna U.
 4HKY
 74.5
 74.34
 70.53
 60.82
 62.7
 69.61





37
 Miguel T.
 4HKY
 85.28
 62.88
 59.27
 50.21
 50.64
 59.21





38
 Seo Kelly K.
 3RKK
 8.73
 26.09
 29.38
 21.15
 21.97
 11.93





39
 Ramiro R.
 4EY2
 74.06
 76.91
 70.46
 65.41
 67.96
 69.15





40
 Priya P.
 4EYL
 73.73
 82.76
 82.54
 72.63
 73.77
 91.35
 81.51
 85.92
 84.55
 74.62
 74.79
 97.04
41
 So-Youn P.
 3Q6X
 80.43
 81.96
 77.29
 67.84
 69.82
 82.84





42
 Daniel D.
 4EYF
 73.27
 77.73
 73.06
 64.84
 66.86
 82.29





43
 Nancy I.
 4EXY
 78.89
 75.23
 70.63
 73.48
 74.21
 38.53





44
 Ariel C.
 3RKJ
 53.40
 35.98
 41.54
 29.62
 32.46
 25.60





45
 Vicky G.
 4EXY
 78.5
 73.07
 68.09
 72.83
 73.81
 38.24
 85.78
 76.31
 71.19
 72.99
 73.28
 40.03
46
 Spencer C.
 4HL1
 72.79
 83.29
 83.08
 75.30
 77.52
 69.16





47
 Stella M.
 4EYL
 75.28
 83.23
 83.07
 73.62
 73.58
 105.56





48
 Jiaqi Z.
 4EYL
 76.58
 83.05
 82.59
 73.95
 72.76
 92.26





49
 Hyun-Young L.
 4EXY
 80.07
 74.45
 71.16
 74.41
 74.09
 38.87






50
 Selena I.
 4EYL
 75.05
 82.23
 82.79
 72.63
 74.18
 91.82





51
 Brandy C.
 4HKY
 85.79
 74.99
 68.49
 65.52
 65.71
 67.37





52
 Renee F.
 4EYL
 75.26
 66.35
 68.88
 54.87
 56.67
 58.53
 84.34
 69.26
 71.12
 59.02
 59.95
 N/A
53
 James T.
 3SBl
 44.94
 46.21
 40.56
 44.79
 40.98
 45.75





54
 Karuna A.
 4HL2
 73.33
 71.9
 88.7
 87.9
 92.23
 79.45





55
 Jacqueline E.
 4HL2
 67.91
 52.52
 59.76
 38.11
 37.55
 63.49
 67.76
 52.56
 59.85
 41.66
 35.80
 63.84
56
 Kevin E. (redo)
 4EYB
 80.93
 80.38
 76.66
 69.89
 69.62
 87.91





57
 Katherine V. (redo)
 3SBL
 48.70
 42.78
 42.78
 45.21
 41.33
 44.95





58
 Gabe H.
 4HL2
 115.04
 80.56
 76.95
 65.54
 66.96
 86.35
 113.25
 85.00
 68.53
 70.53
 69.24
 91.88
59
 Brian C.
 3Q6X
 80.26
 59.67
 76.41
 67.67
 70.41
 82.39





60
 Salil D.
 4EYB
 77.28
 78.37
 70.60
 66.56
 67.08
 80.15






Binding DB Info: (To Be Done)

http://www.bindingdb.org/bind/index.jsp
search for "Metallo-beta-lactamase"

Download Binding DB compounds using the 'Computed 3D by Vconf -m prep' option (Does not work)







REFERENCES:

An altered zinc-binding site confers resistance to a covalent inactivator of New Delhi metallo-beta-lactamase-1 (NDM-1) discovered by high-throughput screening.
Thomas PW, Spicer T, Cammarata M, Brodbelt JS, Hodder P, Fast W. Bioorg Med Chem. 2013 Mar 29. doi:pii: S0968-0896(13)00245-9. 10.1016/j.bmc.2013.03.031. [Epub ahead of print]
PMID: 23591260

Characterization of purified New Delhi metallo-β-lactamase-1.
Thomas PW, Zheng M, Wu S, Guo H, Liu D, Xu D, Fast W. Biochemistry. 2011 Nov 22;50(46):10102-13. doi: 10.1021/bi201449r. Epub 2011 Nov 1.
PMID: 22029287
Related citations Remove from clipboard
Kim, Y., Cunningham, M. A., Mire, J., Tesar, C., Sacchettini, J. & Joachimiak, A. NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism. FASEB J. 27, Epub ahead of print (2013).
King, D. T., Worrall, L. J., Gruninger, R. & Strynadka, N. C. J. New Delhi metallo-β- lactamase: structural insights into β-lactam recognition and inhibition. JACS 134, 11362-11365 (2012).


Metallo Beta-Lactamase GOLD docking paper (NOT New Delhi version though) - 071613 JTB
http://www.ncbi.nlm.nih.gov/pubmed/16378729